| fastq10x_qc_analysis |
1 |
- results/fastq10x/fastq10x_qc_analysis.ipynb
- results/fastq10x/fastq10x_qc_analysis.html
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| align_fastq10x_summary |
1 |
- results/aligned_fastq10x/align_fastq10x_summary.ipynb
- results/aligned_fastq10x/align_fastq10x_summary.html
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| viral_fastq10x_coverage |
1 |
- results/viral_fastq10x/viraltag_locs.csv
- results/viral_fastq10x/viralbc_locs.csv
- results/viral_fastq10x/viral_fastq10x_coverage.ipynb
- results/viral_fastq10x/viral_fastq10x_coverage.html
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| count_viraltags_fastq10x |
1 |
- results/viral_fastq10x/count_viraltags_fastq10x-wt_virus_pilot.ipynb
- results/viral_fastq10x/count_viraltags_fastq10x-wt_virus_pilot.html
- results/viral_fastq10x/wt_virus_pilot_viraltag_counts.csv
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| analyze_cell_gene_matrix |
1 |
- results/analysis/wt_virus_pilot_analyze_cell_gene_matrix.ipynb
- results/analysis/wt_virus_pilot_analyze_cell_gene_matrix.html
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| make_fastq10x |
1 |
- results/fastq10x/wt_virus_pilot-2019-12-03_all_R1.fastq.gz
- results/fastq10x/wt_virus_pilot-2019-12-03_all_R2.fastq.gz
- results/fastq10x/mkfastq_output/wt_virus_pilot-2019-12-03
- results/fastq10x/wt_virus_pilot-2019-12-03_qc_stats.csv
- _mkfastq_wt_virus_pilot-2019-12-03.csv
- __wt_virus_pilot-2019-12-03.mro
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| align_fastq10x |
1 |
- results/aligned_fastq10x/wt_virus_pilot/Solo.out/Gene/Summary.csv
- results/aligned_fastq10x/wt_virus_pilot/Solo.out/Gene/UMIperCellSorted.txt
- results/aligned_fastq10x/wt_virus_pilot/Solo.out/Gene/filtered/matrix.mtx
- results/aligned_fastq10x/wt_virus_pilot/Solo.out/Gene/filtered/features.tsv
- results/aligned_fastq10x/wt_virus_pilot/Solo.out/Gene/filtered/barcodes.tsv
- results/aligned_fastq10x/wt_virus_pilot/Aligned.sortedByCoord.out.bam
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| index_bam |
1 |
- results/aligned_fastq10x/wt_virus_pilot/Aligned.sortedByCoord.out.bam.bai
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| samtools index {input} {output}
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| get_cb_whitelist_10x |
1 |
- results/aligned_fastq10x/cb_whitelist_10x.txt
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| if [[ {params.url} == *.gz ]]
then
wget -O - {params.url} | gunzip -c > {output}
else
wget -O - {params.url} > {output}
fi
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| make_refgenome |
1 |
- results/genomes/cell_and_virus_gtf.gtf
- results/genomes/refgenome
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| cat {input.cell_gtf} {input.viral_gtf} > {output.concat_gtf}
mkdir -p {output.genomeDir}
STAR --runThreadN {threads} --runMode genomeGenerate --genomeDir {output.genomeDir} --genomeFastaFiles {input.cell_genome} {input.viral_genome} --sjdbGTFfile {output.concat_gtf}
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| get_cell_genome |
1 |
- results/genomes/cell_genome.fasta
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| wget -O - {params.ftp} | gunzip -c > {output}
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| get_cell_gtf |
1 |
- results/genomes/cell_gtf.gtf
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| wget -O - {params.ftp} | gunzip -c > {output}
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